Hi!
I am running my RNAseq data set with Tophat 2.0.3 and 2.0.4 and I got a fail when Bowtie start to map the "left_kept_reads" into the genome.
[2012-07-18 18:00:00] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-18 18:00:00] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-07-18 18:00:00] Checking for Samtools
Samtools version: 0.1.18.0
[2012-07-18 18:00:00] Checking for Bowtie index files
[2012-07-18 18:00:00] Checking for reference FASTA file
[2012-07-18 18:00:00] Generating SAM header for /home/volatile/tefa/Programas/bowtie2-2.0.0-beta5/indexes/Danio_rerio.Zv9.60.dna.toplevel
format: fastq
quality scale: phred33 (default)
[2012-07-18 18:00:03] Preparing reads
left reads: min. length=100, max. length=100, 46097947 kept reads (753470 discarded)
right reads: min. length=100, max. length=100, 46737157 kept reads (114260 discarded)
[2012-07-18 18:47:19] Mapping left_kept_reads to genome Danio_rerio.Zv9.60.dna.toplevel with Bowtie2
/home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/bam2fastx: /usr/lib64/libz.so.1: no version information available (required by /home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/bam2fastx)
/home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/fix_map_ordering: /usr/lib64/libz.so.1: no version information available (required by /home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/fix_map_ordering)
Line 91407353, sequence length 74 vs 100 from CIGAR
Parse error at line 91407353: CIGAR and sequence length are inconsistent
[FAILED]
Error running bowtie:
That's weird, because I didn't get this error when I run the same data set with Tophat 2.0.0.....The version 2.0.0 works well
Anyone have an idea to solve it????
TEFA
I am running my RNAseq data set with Tophat 2.0.3 and 2.0.4 and I got a fail when Bowtie start to map the "left_kept_reads" into the genome.
[2012-07-18 18:00:00] Beginning TopHat run (v2.0.4)
-----------------------------------------------
[2012-07-18 18:00:00] Checking for Bowtie
Bowtie version: 2.0.0.5
[2012-07-18 18:00:00] Checking for Samtools
Samtools version: 0.1.18.0
[2012-07-18 18:00:00] Checking for Bowtie index files
[2012-07-18 18:00:00] Checking for reference FASTA file
[2012-07-18 18:00:00] Generating SAM header for /home/volatile/tefa/Programas/bowtie2-2.0.0-beta5/indexes/Danio_rerio.Zv9.60.dna.toplevel
format: fastq
quality scale: phred33 (default)
[2012-07-18 18:00:03] Preparing reads
left reads: min. length=100, max. length=100, 46097947 kept reads (753470 discarded)
right reads: min. length=100, max. length=100, 46737157 kept reads (114260 discarded)
[2012-07-18 18:47:19] Mapping left_kept_reads to genome Danio_rerio.Zv9.60.dna.toplevel with Bowtie2
/home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/bam2fastx: /usr/lib64/libz.so.1: no version information available (required by /home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/bam2fastx)
/home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/fix_map_ordering: /usr/lib64/libz.so.1: no version information available (required by /home/volatile/tefa/Programas/tophat-2.0.4.Linux_x86_64/fix_map_ordering)
Line 91407353, sequence length 74 vs 100 from CIGAR
Parse error at line 91407353: CIGAR and sequence length are inconsistent
[FAILED]
Error running bowtie:
That's weird, because I didn't get this error when I run the same data set with Tophat 2.0.0.....The version 2.0.0 works well
Anyone have an idea to solve it????
TEFA
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